The active sites of enzymes are contained within nanoscale environments that exhibit exquisite levels of specificity to particular molecules. The development of such nanoscale environments on synthetic surfaces, which would be capable of discriminating between molecules that would nominally bind in a similar way to the surface, could be of use in nanosensing, selective catalysis and gas separation. However, mimicking such subtle behaviour, even crudely, with a synthetic system remains a significant challenge. Here, we show that the reactive sites on the surface of a tetrairidium cluster can be controlled by using three calixarene-phosphine ligands to create a selective nanoscale environment at the metal surface. Each ligand is 1.4 nm in length and envelopes the cluster core in a manner that discriminates between the reactivities of the basal-plane and apical iridium atoms. CO ligands are initially present on the clusters and can be selectively removed from the basal-plane sites by thermal dissociation and from the apical sites by reactive decarbonylation with the bulky reactant trimethylamine-N-oxide. Both steps lead to the creation of metal sites that can bind CO molecules, but only the reactive decarbonylation step creates vacancies that are also able to bond to ethylene, and catalyse its hydrogenation.